[gmx-users] problem with make_ndx
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 1 12:34:20 CET 2012
Anushree Tripathi wrote:
> But in coordinate file(.pdb file) ,I am not getting the atoms which
> belongs to DPPC.only I have included the name of dppc.itp file like this:
This is precisely the problem - you have no DPPC in the coordinate file.
> ;Include DPPC chain topology
> #include "dppc.itp"
Adding information to the topology has no effect on the coordinate file.
Consult the membrane protein tutorial for how to properly build such a system.
> That's why I have found the atoms wich belongs to DPPC molecule from
> dppc.itp file itself.
> On Wed, Feb 1, 2012 at 12:40 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> On 1/02/2012 6:04 PM, Anushree Tripathi wrote:
>> When I run the command (i.e., make_ndx -f em.gro -o index.ndx) ,it
>> is showing the following options:
>> 0 System : 18379 atoms
>> 1 Protein : 11739 atoms
>> 2 Protein-H : 9135 atoms
>> 3 C-alpha : 1173 atoms
>> 4 Backbone : 3519 atoms
>> 5 MainChain : 4693 atoms
>> 6 MainChain+Cb : 5773 atoms
>> 7 MainChain+H : 5842 atoms
>> 8 SideChain : 5897 atoms
>> 9 SideChain-H : 4442 atoms
>> 10 Prot-Masses : 11739 atoms
>> 11 non-Protein : 6640 atoms
>> 12 Water : 6636 atoms
>> 13 SOL : 6636 atoms
>> 14 non-Water : 11743 atoms
>> 15 Ion : 4 atoms
>> 16 CL : 4 atoms
>> 17 Water_and_ions : 6640 atoms
> So your system has 18K atoms, with 11K protein and the rest solvent
> and ions. As Justin suggested, this coordinate file does not have
> DPPC in it.
>> for my work, I used 16|13 then 1|11.lastly I saved it using
>> 'q'.But there is no option for DPPC (as given in tutorial we have
>> to merge protein with DPPC).After runing the command (grompp -f
>> nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr),it is
>> showing error:
>> Group DPPC not found in indexfile.
>> Maybe you have non-default goups in your mdp file, while not using
>> the '-n' option of grompp.
>> In that case use the '-n' option.
>> To troubleshoot the error,I have kept one more group in index.ndx
>> file with number of atoms which I found from dppc.itp file(at the
>> end of file) like this
>> 1 2 3 4 5 6 7 8 9 10 11 12 13
>> 14 15
>> 16 17 18 19 20 21 22 23 24 25 26 27 28
>> 29 30
>> 31 32 33 34 35 36 37 38 39 40 41 42 43
>> 44 45
>> 46 47 48 49 50
> These numbers have to reference the atom numbers in the coordinate
> file, not the [moleculetype]. Since you've done the latter, you get
> the problem with T-coupling groups. But go back and use a coordinate
> file that actually has DPPC in it.
>> Again after running the grompp command (grompp -f nvt.mdp -c
>> em.gro -p topol.top -n index.ndx -o nvt.tpr),I am getting the
>> following error:
>> Atom 1 in multiple T-Coupling groups (1 and 2).
>> Please suggest me the reason as well as solution for this problem.
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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